From Knut.Reinert@fu-berlin.de Thu Sep 17 08:57:18 2009 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MoAvc-0006Nz-UM>; Thu, 17 Sep 2009 08:57:17 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1MoAvR-0008HG-6Z>; Thu, 17 Sep 2009 08:57:05 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1MoAvR-0000NV-01>; Thu, 17 Sep 2009 08:57:05 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Thu, 17 Sep 2009 08:57:05 +0200 From: "Reinert, Knut" To: "carsten.kemena@crg.es" , "cedric.notredame@crg.es" , "Andreas.Keller@febit.de" , "j.roehr@fu-berlin.de" , "trappe@inf.fu-berlin.de" , Knut Reinert , David Weese , "bkehr@zedat.fu-berlin.de" , "rausch@inf.fu-berlin.de" , "vipul.patel@web.de" , "pyl@inf.fu-berlin.de" , =?iso-8859-1?Q?Robert_Wei=DFmann?= , "juergen.kleffe@charite.de" , Markus Bauer , "BBarnes@illumina.com" , "TMann@illumina.com" , "christoph.dieterich@mdc-berlin.de" , =?iso-8859-1?Q?Andreas_D=F6ring?= , "matthias.dodt@mdc-berlin.de" , Anne-Katrin Emde , "krugel@in.tum.de" , "antonio.espinosa@caos.uab.es" , "fcores@diei.udl.cat" , "orobitg@diei.udl.cat" , "szillus@informatik.uni-tuebingen.de" , "fischer@informatik.uni-tuebingen.de" , Patrick May Date: Thu, 17 Sep 2009 08:56:00 +0200 Thread-Topic: New SeqAn release 1.2 / SeqAn retreat info Thread-Index: Aco3ZBARj0PDhtQ/RxuRQT8MbY2C7Q== Message-ID: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: multipart/alternative; boundary="_000_F0C562F5B46442CD9BC57105A4A982BCfuberlinde_" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-ID: 151147::1253170636-00000A7C-6CD0D77A/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.027516, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Kenia.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.6 required=5.0 tests=ALL_TRUSTED,HTML_FONT_BIG, HTML_MESSAGE X-Mailman-Approved-At: Thu, 17 Sep 2009 08:59:52 +0200 Cc: "seqan-dev@lists.fu-berlin.de" , "Kasseckert, Anja" Subject: [Seqan-dev] New SeqAn release 1.2 / SeqAn retreat info X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 17 Sep 2009 06:57:18 -0000 --_000_F0C562F5B46442CD9BC57105A4A982BCfuberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear SeqAn retreat participants, The SeqAn team is happy to welcome you to Berlin. As announced in the invitation we will start on Monday with a Tutorial on S= eqAn. Hence we would like to ask you to install the latest SeqAn release (1.2) do= wnloadable from the SeqAn website (www.seqan.de) and install it on your l= aptop. You can develop programs in SeqAn under Windows, Unix, or MacOS X. Also, using Cmake you can generate make files for the demos using your pref= erred IDE. Please see the installation instructions on the website for more details Try to install SeqAn and compile the demos. If you do not succeed do not wo= rry we will assist you on Monday. See you in Berlin on Monday in Room 006, Computer Science building, Takusst= rasse 9, 9 am. The SeqAn team =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 09:00-09:45 Introduction to SeqAn and the retreat (Knut Reinert) 09:45-10:30 SeqAn design principles (Andreas Gogol-D=F6ring) 10:30-10:45 Coffee break 10:45-13:00 Practical tutorial Part I: Small tasks applying design princip= les (SeqAn Team) 13:00-14:00 Lunch 14:00-15:45 Practical tutorial Part II: Small tasks applying design princip= le (SeqAn Team) 15:45-16:45 SeqAn Content (David Weese) 16:45-17:00 Coffee break 17:00-17:30 Advanced example (Anne Katrin-Emde) 17:30-18:40: transfer to Berlin-Kreuzberg and Illumina dinner on board of a= cruise ship =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D --_000_F0C562F5B46442CD9BC57105A4A982BCfuberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear SeqAn retreat participants,

The S= eqAn team is happy to welcome you to Berlin.

As an= nounced in the invitation we will start on Monday with a Tutorial on SeqAn.=

Hence we would like to ask you to install the lat= est SeqAn release (1.2) downloadable from the
SeqAn website (www.seqan.de) and install it on your lapto= p.

You can develop programs in SeqAn under Windows= , Unix, or MacOS X.
Also, using Cmake you can generate make files= for the demos using your preferred IDE.
Please see the inst= allation instructions on  the website for more details
Try t= o install SeqAn and compile the demos. If you do not succeed do not worry w= e will assist you on Monday.

See you in Berlin on = Monday in Room 006, Computer Science building, Takusstrasse 9,  9 am.<= /div>

The SeqAn team

=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

<= span style=3D"letter-spacing: 0px; ">09:00-09= :45  Introduction to SeqAn  and the retreat  (Knut Reinert)<= /span>
09:45-10:30  SeqAn design principles (Andreas Gogol-D=F6ring)
10= :30-10:45  Coffee break
10:45-13:00  Practical tutorial Part I: Small ta= sks applying design principles (SeqAn Team)

13:00-14:00 Lunch
14:00-15:45 Practical= tutorial Part II: Small tasks applying design principle (SeqAn Team)
15:45-16:45 S= eqAn Content (David Weese) 
16:45-17:00 Coffee break
17:00-17:30 Advanced example (A= nne Katrin-Emde) 

17:30-18:40: transfer to Berli= n-Kreuzberg and Illumina dinner on board of a cruise ship

=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
= --_000_F0C562F5B46442CD9BC57105A4A982BCfuberlinde_-- From joinass.armada@email.it Tue Sep 22 13:04:06 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Mq3AB-0007el-Nx>; Tue, 22 Sep 2009 13:04:03 +0200 Received: from smtp-out05.email.it ([212.97.34.16]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Mq3AB-0001fH-JY>; Tue, 22 Sep 2009 13:04:03 +0200 Received: from localhost (localhost.localdomain [127.0.0.1]) by smtp-out05.email.it (Postfix) with ESMTP id 897614031 for ; Tue, 22 Sep 2009 13:03:58 +0200 (CEST) Received: from smtp-out05.email.it ([127.0.0.1]) by localhost (smtp-out05.email.it [127.0.0.1]) (amavisd-new, port 10024) with LMTP id yUoZFee3pyfk for ; Tue, 22 Sep 2009 13:03:58 +0200 (CEST) Received: from 79.44.240.48 (wm9.email.it [212.97.34.52]) by smtp-out05.email.it (Postfix) with ESMTP id 64BCD4003 for ; Tue, 22 Sep 2009 13:03:58 +0200 (CEST) Received: from Email-mailer ([79.44.240.48]) by 79.44.240.48 with HTTP (Wmail); Tue, 22 Sep 2009 13:04:00 +0200 Date: Tue, 22 Sep 2009 13:04:00 +0200 To: seqan-dev@lists.fu-berlin.de From: joinass.armada@email.it Message-ID: <2df28fc5c689bdf4485d69d4fb14806f@79.44.240.48> X-Priority: X-Mailer: Webmail-Email.it [Mailer version 1.70] X-SenderIP: 79.44.240.48 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="b1_2df28fc5c689bdf4485d69d4fb14806f" X-Originating-IP: 212.97.34.16 X-ZEDAT-Hint: A X-purgate: clean X-purgate-ID: 151147::1253617443-00000A7C-FFA746C5/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.004283, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Niger.ZEDAT.FU-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.5 required=5.0 tests=FORGED_RCVD_HELO,HTML_30_40, HTML_MESSAGE,NO_REAL_NAME,RCVD_BY_IP,RCVD_HELO_IP_MISMATCH, RCVD_NUMERIC_HELO Subject: [Seqan-dev] HammingHorspool X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: joinass.armada@email.it, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 22 Sep 2009 11:04:06 -0000 --b1_2df28fc5c689bdf4485d69d4fb14806f Content-Type: text/plain; charset = "iso-8859-1" Content-Transfer-Encoding: 8bit Hi, the following code: Pattern< String<char> ,seqan::HammingHorspool> pattern(needle,1); generates this error: Error    23    error C2440: 'return': conversion impossible from 'const seqan::String<TValue,TSpec>' to 'seqan::String<TValue,TSpec> &'    E:\Seqan_Release_1.2\seqan\find\find_pattern_base.h    291 Note:I have uncomment #include <seqan/find/find_hamming_horspool.h> in find.h Have you any idea to solve this problem? Thanks Rey -- Caselle da 1GB, trasmetti allegati fino a 3GB e in piu' IMAP, POP3 e SMTP autenticato? GRATIS solo con Email.it: http://www.email.it/f Sponsor: L'Hotel Sarti propone pacchetti per il benessere e il relax: fino a novembre se prenoti 12 gionri ne paghi solo 11, con il soggiorno di una settimana, ma inferiore ai 12 giorni, si usufruisce dello sconto del 5% , supplemento camera singola Euro 10 al giorno! Clicca qui: http://adv.email.it/cgi-bin/foclick.cgi?mid=9619&d=20090922 --b1_2df28fc5c689bdf4485d69d4fb14806f Content-Type: text/html; charset = "iso-8859-1" Content-Transfer-Encoding: 8bit Hi,

the following code:

Pattern< String<char> ,seqan::HammingHorspool> pattern(needle,1);

generates this error:

Error    23    error C2440: 'return': conversion impossible from 'const seqan::String<TValue,TSpec>' to 'seqan::String<TValue,TSpec> &'    E:Seqan_Release_1.2seqanfindfind_pattern_base.h    291

Note:I have uncomment #include <seqan/find/find_hamming_horspool.h> in find.h

Have you any idea to solve this problem?


Thanks

Rey
----
Caselle da 1GB, trasmetti allegati fino a 3GB e in piu' IMAP, POP3 e SMTP autenticato? GRATIS solo con Email.it

Sponsor:
L'Hotel Sarti propone pacchetti per il benessere e il relax: fino a novembre se prenoti 12 gionri ne paghi solo 11, con il soggiorno di una settimana, ma inferiore ai 12 giorni, si usufruisce dello sconto del 5% , supplemento camera singola Euro 10 al giorno!
Clicca qui
--b1_2df28fc5c689bdf4485d69d4fb14806f-- From j.reid@mail.cryst.bbk.ac.uk Mon Sep 28 11:48:43 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MsCqY-0001po-Tt>; Mon, 28 Sep 2009 11:48:42 +0200 Received: from adora-ext.cryst.bbk.ac.uk ([193.61.32.13] helo=adora.cryst.bbk.ac.uk) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MsCqY-0007ow-PU>; Mon, 28 Sep 2009 11:48:42 +0200 Received: from [127.0.0.1] (axon-ext.cryst.bbk.ac.uk [193.61.32.77]) by adora.cryst.bbk.ac.uk (8.13.8/8.13.8) with ESMTP id n8S9paRk030462 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO) for ; Mon, 28 Sep 2009 10:51:39 +0100 Message-ID: <4AC0865F.8020603@mail.cryst.bbk.ac.uk> Date: Mon, 28 Sep 2009 10:48:15 +0100 From: John Reid User-Agent: Thunderbird 2.0.0.23 (X11/20090817) MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Cryst-BBK-MailScanner-Information: Please contact CCSG for more information (http://www. cryst.bbk.ac.uk/CCSG) X-Cryst-BBK-MailScanner-ID: n8S9paRk030462 X-Cryst-BBK-MailScanner: Found to be clean X-Cryst-BBK-MailScanner-SpamCheck: not spam, SpamAssassin (not cached, score=0, required 5, autolearn=not spam) X-Cryst-BBK-MailScanner-From: j.reid@mail.cryst.bbk.ac.uk X-Cryst-BBK-MailScanner-Watermark: 1254736300.06286@str9Bdf7S75DIX1bX11iVw X-Originating-IP: 193.61.32.13 X-purgate: clean X-purgate-ID: 151147::1254131322-00000A7C-0C3F7D17/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.271017, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] Top down iteration bug X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 28 Sep 2009 09:48:44 -0000 Could someone check if ticket 93 is as serious a bug as I think it is? http://trac.mi.fu-berlin.de/seqan/ticket/93 It has been open for 3 months now Thanks, John. From weese@inf.fu-berlin.de Tue Sep 29 14:22:01 2009 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MsbiS-0000Ol-8e>; Tue, 29 Sep 2009 14:22:00 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MsbiS-0004Fm-7D>; Tue, 29 Sep 2009 14:22:00 +0200 Received: from [160.45.118.25] (helo=blowfish.mi.fu-berlin.de) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1MsbiS-0002N9-52>; Tue, 29 Sep 2009 14:22:00 +0200 Message-ID: <4AC1FBE8.6050601@inf.fu-berlin.de> Date: Tue, 29 Sep 2009 14:22:00 +0200 From: David Weese User-Agent: Thunderbird 2.0.0.23 (Macintosh/20090812) MIME-Version: 1.0 To: SeqAn Development References: <4AC0865F.8020603@mail.cryst.bbk.ac.uk> In-Reply-To: <4AC0865F.8020603@mail.cryst.bbk.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.118.25 X-purgate: clean X-purgate-ID: 151147::1254226920-00000A7C-0E057802/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.019079, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Top down iteration bug X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 29 Sep 2009 12:22:01 -0000 Hi John, sorry, I simply was snowed under with work. I could narrow down the bug to a fasta file of sequence 12 and 58 (counting starts at 0). Something is wrong with the lcp-Value of suffix 852 of seq12 ("AAA") and 771 of seq58 ("A"). The lcp-Value is 3 instead of 1, therefore the suffix tree is also wrong. I think problem is either the suffix array or the lcp table construction. I'm investigating. Cheers, David John Reid schrieb: > Could someone check if ticket 93 is as serious a bug as I think it is? > > http://trac.mi.fu-berlin.de/seqan/ticket/93 > > It has been open for 3 months now > > Thanks, > John. > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From weese@inf.fu-berlin.de Wed Sep 30 00:04:23 2009 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Msko1-0002m2-IC>; Wed, 30 Sep 2009 00:04:21 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Msko1-0007gm-Gl>; Wed, 30 Sep 2009 00:04:21 +0200 Received: from imp053122.vpn.mi.fu-berlin.de ([130.133.53.122]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1Msko1-00078z-ED>; Wed, 30 Sep 2009 00:04:21 +0200 Message-ID: <4AC2846C.10606@inf.fu-berlin.de> Date: Wed, 30 Sep 2009 00:04:28 +0200 From: David Weese User-Agent: Thunderbird 2.0.0.23 (Macintosh/20090812) MIME-Version: 1.0 To: SeqAn Development References: <4AC0865F.8020603@mail.cryst.bbk.ac.uk> In-Reply-To: <4AC0865F.8020603@mail.cryst.bbk.ac.uk> X-Enigmail-Version: 0.96.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit X-Originating-IP: 130.133.53.122 X-purgate: clean X-purgate-ID: 151147::1254261861-00000A7C-1D3207D0/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Kenia.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Top down iteration bug X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 29 Sep 2009 22:04:23 -0000 Hi John, I just fixed this bug. For details see: https://trac.mi.fu-berlin.de/seqan/ticket/93 Sorry for the delay. Cheers, David John Reid schrieb: > Could someone check if ticket 93 is as serious a bug as I think it is? > > http://trac.mi.fu-berlin.de/seqan/ticket/93 > > It has been open for 3 months now > > Thanks, > John. > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev